Hi Dusan,
Thank you for the details, it helps a lot.
The issue is caused by unintended HTML code, which is not coming from the plugin. See this screenshot of the final page output: https://i.imgur.com/oJDEina.png
There are line breaks added for the empty line codes, which then push the input field.
This usually happens when the plugin shortcode is used in a text block of some sort, which converts text to HTML, so line breaks, empty lines etc.. are wrapped by extra HTML tags. My guess is, that in the new release there is a slightly different indentation, and more unwanted HTML is added by the formatter.
If you use a widget or a block of some sort to hold the search shortcode, make sure to switch it to a shortcode or HTML block instead of a plain text block, so indentaion is not converted to HTML tags.